Protein Folding Theory

Proteins are essential to organisms and many processes that keep people functioning and living every day. Proteins are comprised of polypeptides that are folded into different forms to fulfill a biological function. Each polypeptide is part of a single, linear chain of amino acids that are bonded by peptide bonds. The amino acid sequence of these polymer chains encodes the sequence of genes. These different genes can code for proteins that make enzymes, muscle structure, and even mechanical functions.

Protein primary structure is composed of amino acid residues. There are 20 different amino acids that can compose this amino acid sequence. The non-covalent interactions and the structure of the peptide bonds in these primary sequences help determine how the protein folds into its secondary structure. The bond’s rotation is characterized by the φ (PHI), ψ (PSI), ω (omega) rotation about the peptide bonds (Figure 1). The secondary structure shows the local spatial arrangement of the polypeptide chain characterized by the α-helix, the β-sheet, the random coil and the β-turn. Unlike the tertiary structure of a protein, these secondary structures do not dictate function. The tertiary structures of a protein fall into two major classes: the fibrous proteins and the globular proteins. The fibrous proteins are usually found with membranes. Globular proteins, on the other hand are typically water-soluble like myoglobin. The tertiary structure of a protein compiles to from the quaternary structure of proteins. The quaternary structure is comprised of multiple tertiary structure proteins forming a larger protein together. The structure can depend on the active site of each domain, the multiple binding sites within the structure...

... middle of paper ...

...actually fold.

Works Cited

1. Arkun, Y., Gur, M. 2012. Combining optimal control theory and molecular dynamics for protein folding. PLoS ONE. 7: e29628 (1-8).

2. Fersht, A.R. 1995. Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications. PNAS. 92: 10869-10873.

3. Karplus, M., Weaver, D.L. 1993. Protein foling dynamics: the diffusion-collision model and experimental data. Protein science. 3: 650-668.

4. Kmiecik, S., Kolinski, A. 2011. Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism. JACS. 133: 10283-10289.

5. Onuchic, J.N., Wolynes, P.G. 2004. Theory of protein folding. Current opinion in structural biology. 14: 70-75.

6. Rose, G.D., Fleming, P.J., Banavar, J.R., Maritan, A. 2006. A backbone-based theory of protein folding. PNAS. 103: 16623-16633.